Either way, Sora is a highly requested character, so there is a chance he will make it in.
I mean Cloud got in. No one saw that coming.
Not sure why Cloud would get in and Sora be denied. I assume Cloud is more popular/well known at least. And perhaps he is easier to portray correctly. Perhaps Nomura didn't want Sora in the previous smash game as KH3 was in development, and the game added a lot more to Sora in terms of appearance/gameplay/etc. And he may have wanted to show Sora in the smash series as up-to-date, thus he may have decided to wait until after KH3, then he could possibly put him in the next smash game.
Anyway, there may be problems (like what has been stated), but there is still a chance.